The president doesn’t have final authority over the EPA. If he tried to exercise that kind of authority, expect talk of “impeachment” next. The same laws that prevent “spoils system” politics protect career bureaucrats.
Who do you think named Lisa Jackson as EPA administrator? The deputy administrator? Craig E. Hooks? etc. etc. etc.
The POTUS doesn't usually have to micro-manage agencies. Obama just named a bunch of green commies to run the cabinet agencies, and a bunch of czars with similar ideology.
They tried to impeach Bill Clinton. but not for firing 80 US attorneys in his first year.